OpenMD

Added svn revision number to build process, incremented minor version
number, corrected a minimizer keyword

Fixing the build and install method for samples in Madelung, RNEMD,
zeolite, SMIPD

Cleanup of unit normal code in Triangle.cpp
SMIPD now call getUnitNormal instead of getNormal.

Install bugs, tweaks of samples

Added preliminary code for Alpha Hull calculation using qhull.
Added preliminary support to SMIPD to support Alpha Hull.
Alpha Hull does not yet add the correct things to triangle to be returned to SMPID. 
Preliminary changes for shadow hamiltonian integrator.
Chages to md files so they will work in openMD. 

more changes to fix build process and divorce ourselves from CVS

removing spurious cutoffGroup lines from default water.md sample files

Almost all of the changes necessary to create OpenMD out of our old
project (OOPSE-4)

adding interface

Relaxed structure at low T to be not so high up on the PE wall.

Adding one RNEMD sample

Adding Madelung energy sample directory with explanatory notes

Adding samples for SMIPD.

doing zeolite sample

Added large quantities of code for convex hull and constant pressure langevin dynamics.

Fixes for Torsions and Inversions, Amber is mostly working now.

Code work on thiols and TraPPE torsions.

Removed accidental print lines.

Added model for thiols.

Added minimizer sample for metal.

Changes....

Added surfaces for Ni and Pd.

Added more surfaces.

Added samples for metal slabs.

Many fixes for Charmm-type torsions.

*** empty log message ***

Broken files on install

Fixed Makefile problems with the samples and added several missing makefiles.

fixed a bug where the pressure tensor wouldn't update for atoms in the switching region when # of atoms in a group = 1

Added md file for half of a icosahedron.

Adding a starter file for the secondary prism {1,1,-2,0} face.

adding new ice surface files

new ideal structures

Added a bunch of bond order parameter test cases.

more openbabel updates, also changing velocitizer to thermalizer to
avoid a filename collision on case-insensitve file systems

Added velocitizer utility program, added samples of its use to the
builder samples.

Adding samples for builders

fixed a few bugs

fixing missing lattice arguments, adding a builder sample

adding builder samples

Fixing the builders to prepare for OOPSE-4 release

converted samples over to the OOPSE-4 file format

Fixed an MPI bug in thermodynamic integration

Massive changes preparing for release of OOPSE-4: The main difference
is that the new MD file format (.md, .dump, .eor) now contains meta-data
information along with the configuration information.

starting change of file formats

Added tred to sample water.md files

removed icc from C++ search lines, did some formatting work
on GB module, mucked around with a GB example

added mpi compilers, demoted pg compilers after pathscale

damping now works for charge-quadrupole and dipole-dipole

testing GB, removing CM drift in Langevin Dynamics, fixing a memory
leak, adding a visitor

Added TIP5P-E and fixed a bug for Thermodynamic integration (you can now have a lambda of 0)

Adding single precision capabilities to c++ side

electrostatic refinement

Removed sqrt splines and shape stuff (doesn't work, so why was it in there?).  Changed some of the water samples to use shifted_force.  Probably should set the defaults to use the damped version now that we sped it up.

Electrosplines added...

splined up sticky

Complete rewrite of spline code and everything that uses it.

Many performance improvements

added a cubic spline to switcheroo

Changes to cutoff radius setting to a more logical procedure - still may change...

Changes in Sutton-Chen units

Missing Makefile in this sample directory

Old makefile.in no longer required

unifying function name in electrostatics

fix make install problem for metals samples

Sutton and Chen should be working now.

Added energy scaling to section parsers.

More Sutton-Chen bug fixes.

Sutton-Chen bug fixes. Almost there...

added files for sutton-chen

More cvs changing.

More moving...

More changes to directory structure.

More Directory changes...

More changing of directory structure

Removed one parasitic argon atom which was living inside the GB
particle.  No alien-like ripping out of the stomach was required.

remove deprecated keywords from samples

removing deprecated nAtoms and nComponents lines

Added Gay-Berne / Argon test case for the cutoff policies

just some parameters

just playing

just playing around - we need to refresh all the samples sometime soon...

playing with switching functions again

playing with switching functions

Just testing...

mmm...  damped shifted force...

added a test molecule

minor changes when testing reaction field

reaction field now works for charges

nothing

added samples for the cutoff methods that Yang Zheng has been working on

added a few GB test cases

Adding samples for gb tests

Adding .md files for GB/LJ tests

Adding some Gay Berne tests

Adding some cutoff tests

added default restraint spring constants into Globals

Testing new cutoff methods

fixing up the samples

just some random changes when testing

fixed some samples

fixing up some samples

turned rf on

fixed up some sample md files

Fixed bugs in reaction field, now it appears as though it really is working...

reaction field seems to work now, still need to do some testing...

just some testing

Equilibrated the sample

Just a longer test

fixed a bug and ran a simulation

Updated tap sample

Included a tap dimer for testing purposes

added a tap example for testing purposes

Modifications to tap.  Also correcting changes to the previous merge that were not caught

Couple of changes for TAP water.  Need to parametrize.

Changed SHED to TAP

OOPSE setup for TAP water.  It's not parametrized, but OOPSE will now let me run it...

Added TIP4P-Ew

Got rid of write statements and am closer to a working shapes

Shapes is limping along with a array bounds overwrite (I think...). At least the parser loads the forcefield fine...

add  Makefile of samples

some samples are not installed correctly

oops...  bad sample

added quadrupole sample

updating samples

messing with samples

oops...  messed up a sample

changes during debug of charge-dipole

forgot a couple of makefiles

added some samples

fixed a bug in MPI restraints

messing with the split dipole test cases

adding test case  of split dipole

Oops...  MPI now builds...

adding test case for split dipole

fixes to restraints

fixing restraints

First commit of the new restraints code

addded a few fun charge-dipole test cases

making some cool test cases

Added ssdrf sample

fixed a sample

oops...

Back to normal... Oh... Restraints should work in parallel now

just some testing changes, I'll return to the original on next commit

working sample

Fun with ice

testing force fields

testing shapes

shorter run

forgot the orientation line

uncommented .in line

adding sample shape directory

fix Makefile under water directory

remove argon.dump and argon.eor from Makefile

Remove some Makefile.in

add Makefile to sample directory

Import of OOPSE v. 2.0